Starting phenix.real_space_refine on Sat Aug 23 22:15:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0i_34412/08_2025/8h0i_34412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0i_34412/08_2025/8h0i_34412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2025/8h0i_34412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2025/8h0i_34412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2025/8h0i_34412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2025/8h0i_34412.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 36 5.49 5 S 80 5.16 5 Cl 2 4.86 5 C 9428 2.51 5 N 2686 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15018 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2797 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1117 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1076 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain breaks: 2 Chain: "E" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1102 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 14, 'rna3p': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 760 SG CYS A 84 62.480 55.613 51.523 1.00 28.54 S ATOM 782 SG CYS A 87 64.206 53.365 53.738 1.00 29.65 S ATOM 2190 SG CYS A 271 22.526 52.111 59.584 1.00152.44 S ATOM 2213 SG CYS A 274 25.489 52.841 58.094 1.00145.84 S Restraints were copied for chains: B, G, H, I, J, Y Time building chain proxies: 3.30, per 1000 atoms: 0.22 Number of scatterers: 15018 At special positions: 0 Unit cell: (147, 113.4, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Cl 2 17.00 S 80 16.00 P 36 15.00 O 2782 8.00 N 2686 7.00 C 9428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 474.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 84 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 240 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 274 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 271 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 87 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS B 240 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 271 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 274 " 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 38.4% alpha, 30.9% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.525A pdb=" N ARG A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.539A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.773A pdb=" N VAL A 148 " --> pdb=" O TRP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 181 through 189 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.606A pdb=" N CYS A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.622A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.808A pdb=" N VAL A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.525A pdb=" N ARG B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.539A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 136 through 148 removed outlier: 3.773A pdb=" N VAL B 148 " --> pdb=" O TRP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.607A pdb=" N CYS B 244 " --> pdb=" O HIS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.622A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.808A pdb=" N VAL B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'C' and resid 14 through 31 removed outlier: 3.514A pdb=" N ILE C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.737A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 15 through 24 removed outlier: 4.087A pdb=" N GLU D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.664A pdb=" N GLY D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 14 through 31 removed outlier: 3.576A pdb=" N LYS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.712A pdb=" N GLU E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 46 " --> pdb=" O HIS E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 46' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.684A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 139 through 150 Processing helix chain 'G' and resid 14 through 31 removed outlier: 3.515A pdb=" N ILE G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 165 through 171 removed outlier: 3.738A pdb=" N LEU G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 15 through 24 removed outlier: 4.088A pdb=" N GLU H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 51 removed outlier: 3.664A pdb=" N GLY H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 140 through 151 Processing helix chain 'I' and resid 14 through 31 removed outlier: 3.576A pdb=" N LYS I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.712A pdb=" N GLU I 45 " --> pdb=" O HIS I 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 46 " --> pdb=" O HIS I 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 42 through 46' Processing helix chain 'I' and resid 99 through 111 Processing helix chain 'I' and resid 165 through 171 removed outlier: 3.684A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 21 Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 139 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 47 removed outlier: 5.028A pdb=" N VAL A 28 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLN A 41 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR A 26 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG A 43 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N LEU A 24 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TRP A 23 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP A 81 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 225 removed outlier: 10.451A pdb=" N ASN A 219 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ARG A 209 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 221 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 260 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N CYS A 291 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 262 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS A 293 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 264 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LYS A 317 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 290 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER A 319 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 292 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 47 removed outlier: 5.029A pdb=" N VAL B 28 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLN B 41 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR B 26 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG B 43 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N LEU B 24 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TRP B 23 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP B 81 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 225 removed outlier: 10.451A pdb=" N ASN B 219 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ARG B 209 " --> pdb=" O ASN B 219 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 221 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR B 260 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N CYS B 291 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 262 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS B 293 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS B 264 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LYS B 317 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 290 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER B 319 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 292 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU C 54 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 53 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU C 54 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 53 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 14.274A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 64 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 55 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 87 removed outlier: 3.766A pdb=" N ILE D 109 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 120 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.471A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 71 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY E 82 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN E 83 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE E 87 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 9 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N TRP E 89 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 13.932A pdb=" N VAL E 7 " --> pdb=" O TRP E 89 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU F 64 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 58 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 28 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 120 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.471A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 71 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY E 82 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N SER E 95 " --> pdb=" O PRO F 100 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE F 102 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU G 54 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU G 54 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.274A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 85 through 87 removed outlier: 3.766A pdb=" N ILE H 109 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.514A pdb=" N VAL J 58 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS J 28 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP J 120 " --> pdb=" O ASP J 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.245A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY I 82 " --> pdb=" O GLY I 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY I 71 " --> pdb=" O GLY I 82 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.245A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2328 1.31 - 1.44: 4902 1.44 - 1.56: 8076 1.56 - 1.69: 72 1.69 - 1.81: 122 Bond restraints: 15500 Sorted by residual: bond pdb=" C ILE G 51 " pdb=" O ILE G 51 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.19e-02 7.06e+03 1.63e+01 bond pdb=" C ILE C 51 " pdb=" O ILE C 51 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.19e-02 7.06e+03 1.53e+01 bond pdb=" C TYR C 69 " pdb=" O TYR C 69 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" C TYR G 69 " pdb=" O TYR G 69 " ideal model delta sigma weight residual 1.234 1.186 0.047 1.26e-02 6.30e+03 1.42e+01 bond pdb=" C TRP G 70 " pdb=" O TRP G 70 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.18e-02 7.18e+03 1.42e+01 ... (remaining 15495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20774 2.05 - 4.09: 312 4.09 - 6.14: 25 6.14 - 8.19: 9 8.19 - 10.23: 4 Bond angle restraints: 21124 Sorted by residual: angle pdb=" N SER C 52 " pdb=" CA SER C 52 " pdb=" C SER C 52 " ideal model delta sigma weight residual 111.28 118.22 -6.94 1.09e+00 8.42e-01 4.05e+01 angle pdb=" N SER G 52 " pdb=" CA SER G 52 " pdb=" C SER G 52 " ideal model delta sigma weight residual 111.28 118.20 -6.92 1.09e+00 8.42e-01 4.03e+01 angle pdb=" N ILE G 51 " pdb=" CA ILE G 51 " pdb=" C ILE G 51 " ideal model delta sigma weight residual 109.34 102.93 6.41 2.08e+00 2.31e-01 9.50e+00 angle pdb=" N ILE C 51 " pdb=" CA ILE C 51 " pdb=" C ILE C 51 " ideal model delta sigma weight residual 109.34 102.98 6.36 2.08e+00 2.31e-01 9.36e+00 angle pdb=" C ILE G 51 " pdb=" CA ILE G 51 " pdb=" CB ILE G 51 " ideal model delta sigma weight residual 111.29 106.29 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 21119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.88: 8838 30.88 - 61.76: 254 61.76 - 92.64: 42 92.64 - 123.52: 0 123.52 - 154.40: 2 Dihedral angle restraints: 9136 sinusoidal: 4138 harmonic: 4998 Sorted by residual: dihedral pdb=" O4' C X 1 " pdb=" C1' C X 1 " pdb=" N1 C X 1 " pdb=" C2 C X 1 " ideal model delta sinusoidal sigma weight residual 200.00 45.60 154.40 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' C Y 1 " pdb=" C1' C Y 1 " pdb=" N1 C Y 1 " pdb=" C2 C Y 1 " ideal model delta sinusoidal sigma weight residual 200.00 45.60 154.40 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" CA TYR I 69 " pdb=" C TYR I 69 " pdb=" N TRP I 70 " pdb=" CA TRP I 70 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2152 0.110 - 0.220: 40 0.220 - 0.329: 2 0.329 - 0.439: 0 0.439 - 0.549: 2 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA SER C 52 " pdb=" N SER C 52 " pdb=" C SER C 52 " pdb=" CB SER C 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CA SER G 52 " pdb=" N SER G 52 " pdb=" C SER G 52 " pdb=" CB SER G 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CA ILE G 51 " pdb=" N ILE G 51 " pdb=" C ILE G 51 " pdb=" CB ILE G 51 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2193 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 70 " 0.022 2.00e-02 2.50e+03 2.35e-02 1.39e+01 pdb=" CG TRP I 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP I 70 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP I 70 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 70 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP I 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 70 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 70 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 70 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP I 70 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 70 " 0.021 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP E 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 70 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP E 70 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 70 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 70 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 70 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 67 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C THR C 67 " -0.038 2.00e-02 2.50e+03 pdb=" O THR C 67 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 68 " 0.013 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 951 2.74 - 3.28: 13899 3.28 - 3.82: 24046 3.82 - 4.36: 28751 4.36 - 4.90: 51337 Nonbonded interactions: 118984 Sorted by model distance: nonbonded pdb=" OG1 THR B 322 " pdb=" OE1 GLU B 325 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 322 " pdb=" OE1 GLU A 325 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN D 46 " pdb=" NH2 ARG D 49 " model vdw 2.261 3.120 nonbonded pdb=" OD1 ASN H 46 " pdb=" NH2 ARG H 49 " model vdw 2.261 3.120 nonbonded pdb=" OD1 ASN A 20 " pdb=" N2 G X 10 " model vdw 2.275 3.120 ... (remaining 118979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.275 15512 Z= 0.213 Angle : 0.605 10.233 21124 Z= 0.339 Chirality : 0.047 0.549 2196 Planarity : 0.004 0.039 2562 Dihedral : 14.234 154.398 5888 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.81 % Allowed : 0.67 % Favored : 98.52 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1654 helix: 1.68 (0.23), residues: 582 sheet: -0.07 (0.26), residues: 404 loop : -0.75 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 222 TYR 0.011 0.001 TYR B 118 PHE 0.013 0.001 PHE A 245 TRP 0.061 0.001 TRP I 70 HIS 0.002 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00310 (15500) covalent geometry : angle 0.60498 (21124) hydrogen bonds : bond 0.14274 ( 684) hydrogen bonds : angle 6.46546 ( 2091) metal coordination : bond 0.11430 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 275 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 281 average time/residue: 0.5759 time to fit residues: 177.2905 Evaluate side-chains 166 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS B 199 HIS ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.072542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.048963 restraints weight = 56416.943| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.94 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15512 Z= 0.272 Angle : 0.702 9.274 21124 Z= 0.361 Chirality : 0.045 0.169 2196 Planarity : 0.005 0.051 2562 Dihedral : 13.124 154.449 2456 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.95 % Allowed : 12.55 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1654 helix: 1.85 (0.22), residues: 578 sheet: 0.16 (0.26), residues: 410 loop : -0.70 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 93 TYR 0.014 0.001 TYR B 111 PHE 0.018 0.002 PHE J 143 TRP 0.035 0.001 TRP E 70 HIS 0.006 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00616 (15500) covalent geometry : angle 0.70194 (21124) hydrogen bonds : bond 0.04379 ( 684) hydrogen bonds : angle 5.05273 ( 2091) metal coordination : bond 0.00868 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8280 (m-80) cc_final: 0.8066 (m-80) REVERT: B 202 TYR cc_start: 0.8289 (m-80) cc_final: 0.8077 (m-80) REVERT: C 36 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9016 (mtmm) REVERT: C 172 ASP cc_start: 0.8965 (p0) cc_final: 0.8682 (p0) REVERT: C 176 LYS cc_start: 0.8994 (pttt) cc_final: 0.8730 (pttt) REVERT: E 14 ASP cc_start: 0.8782 (t0) cc_final: 0.8235 (t0) REVERT: E 105 GLN cc_start: 0.9505 (mm110) cc_final: 0.9276 (mm-40) REVERT: E 171 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: F 114 ILE cc_start: 0.9400 (pt) cc_final: 0.9047 (mt) REVERT: G 36 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9011 (mtmm) REVERT: G 172 ASP cc_start: 0.8960 (p0) cc_final: 0.8667 (p0) REVERT: G 176 LYS cc_start: 0.8993 (pttt) cc_final: 0.8729 (pttt) REVERT: I 14 ASP cc_start: 0.8779 (t0) cc_final: 0.8372 (t0) REVERT: I 37 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8105 (p0) REVERT: I 105 GLN cc_start: 0.9478 (mm110) cc_final: 0.9246 (mm-40) REVERT: I 171 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7879 (pm20) outliers start: 29 outliers final: 10 residues processed: 191 average time/residue: 0.5845 time to fit residues: 122.4262 Evaluate side-chains 171 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 chunk 104 optimal weight: 0.0470 chunk 62 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 145 optimal weight: 0.0050 chunk 27 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 2.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 GLN E 6 GLN F 45 GLN F 77 GLN F 117 GLN G 97 GLN J 45 GLN J 74 GLN J 117 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.073674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.050163 restraints weight = 55807.746| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.96 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15512 Z= 0.141 Angle : 0.628 8.183 21124 Z= 0.318 Chirality : 0.043 0.156 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.016 154.685 2456 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 13.76 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1654 helix: 1.89 (0.22), residues: 578 sheet: 0.31 (0.26), residues: 410 loop : -0.65 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.010 0.001 TYR C 69 PHE 0.016 0.001 PHE J 143 TRP 0.019 0.001 TRP E 70 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00318 (15500) covalent geometry : angle 0.62761 (21124) hydrogen bonds : bond 0.03424 ( 684) hydrogen bonds : angle 4.68821 ( 2091) metal coordination : bond 0.00345 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9239 (ttp) REVERT: A 202 TYR cc_start: 0.8293 (m-80) cc_final: 0.8016 (m-80) REVERT: B 135 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9241 (ttp) REVERT: B 202 TYR cc_start: 0.8286 (m-80) cc_final: 0.8013 (m-80) REVERT: C 2 GLU cc_start: 0.8536 (pm20) cc_final: 0.8257 (pm20) REVERT: C 36 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9027 (mtmm) REVERT: D 98 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8697 (ttmm) REVERT: D 149 ARG cc_start: 0.8405 (tpm170) cc_final: 0.8164 (ttp-170) REVERT: E 105 GLN cc_start: 0.9532 (mm110) cc_final: 0.9249 (mm-40) REVERT: F 114 ILE cc_start: 0.9479 (pt) cc_final: 0.9069 (mt) REVERT: G 2 GLU cc_start: 0.8538 (pm20) cc_final: 0.8258 (pm20) REVERT: G 36 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9029 (mtmm) REVERT: H 98 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8701 (ttmm) REVERT: H 149 ARG cc_start: 0.8366 (tpm170) cc_final: 0.8134 (ttp-170) REVERT: I 14 ASP cc_start: 0.8656 (t0) cc_final: 0.8335 (t0) REVERT: I 105 GLN cc_start: 0.9522 (mm110) cc_final: 0.9307 (mm-40) outliers start: 34 outliers final: 11 residues processed: 190 average time/residue: 0.5264 time to fit residues: 110.5523 Evaluate side-chains 170 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 74 GLN Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 63 optimal weight: 50.0000 chunk 158 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 166 GLN D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.071958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.048285 restraints weight = 56296.826| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.97 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15512 Z= 0.232 Angle : 0.656 8.364 21124 Z= 0.334 Chirality : 0.044 0.147 2196 Planarity : 0.004 0.054 2562 Dihedral : 13.102 156.924 2456 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.15 % Allowed : 15.23 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1654 helix: 1.90 (0.22), residues: 580 sheet: 0.37 (0.26), residues: 408 loop : -0.56 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 148 TYR 0.020 0.001 TYR F 85 PHE 0.015 0.002 PHE D 143 TRP 0.022 0.001 TRP E 70 HIS 0.004 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00527 (15500) covalent geometry : angle 0.65573 (21124) hydrogen bonds : bond 0.03615 ( 684) hydrogen bonds : angle 4.70704 ( 2091) metal coordination : bond 0.00621 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.9311 (ttp) REVERT: A 202 TYR cc_start: 0.8236 (m-80) cc_final: 0.7950 (m-80) REVERT: A 321 MET cc_start: 0.8772 (mpp) cc_final: 0.8281 (mmm) REVERT: B 135 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.9302 (ttp) REVERT: B 202 TYR cc_start: 0.8243 (m-80) cc_final: 0.7957 (m-80) REVERT: B 321 MET cc_start: 0.8767 (mpp) cc_final: 0.8279 (mmm) REVERT: C 2 GLU cc_start: 0.8569 (pm20) cc_final: 0.8330 (pm20) REVERT: C 36 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9023 (mtmm) REVERT: D 98 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8719 (ttmm) REVERT: D 148 ARG cc_start: 0.9165 (tpm170) cc_final: 0.8162 (tpm170) REVERT: E 14 ASP cc_start: 0.8609 (t0) cc_final: 0.8192 (t0) REVERT: E 105 GLN cc_start: 0.9568 (mm110) cc_final: 0.9335 (mm-40) REVERT: F 114 ILE cc_start: 0.9453 (pt) cc_final: 0.9038 (mt) REVERT: G 2 GLU cc_start: 0.8564 (pm20) cc_final: 0.8326 (pm20) REVERT: G 36 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9021 (mtmm) REVERT: H 98 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8723 (ttmm) REVERT: H 148 ARG cc_start: 0.9147 (tpm170) cc_final: 0.8110 (tpm170) REVERT: I 91 LYS cc_start: 0.8894 (tptp) cc_final: 0.8679 (tptp) REVERT: I 105 GLN cc_start: 0.9554 (mm110) cc_final: 0.9314 (mm-40) outliers start: 32 outliers final: 17 residues processed: 181 average time/residue: 0.5286 time to fit residues: 105.5981 Evaluate side-chains 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 chunk 87 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.072460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.048881 restraints weight = 55962.469| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.02 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15512 Z= 0.156 Angle : 0.627 8.762 21124 Z= 0.316 Chirality : 0.042 0.149 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.018 157.184 2456 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.62 % Allowed : 14.70 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.21), residues: 1654 helix: 1.96 (0.22), residues: 582 sheet: 0.28 (0.25), residues: 418 loop : -0.39 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 19 TYR 0.010 0.001 TYR C 69 PHE 0.010 0.001 PHE D 143 TRP 0.015 0.001 TRP E 70 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00356 (15500) covalent geometry : angle 0.62726 (21124) hydrogen bonds : bond 0.03218 ( 684) hydrogen bonds : angle 4.49584 ( 2091) metal coordination : bond 0.00360 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8242 (m-80) cc_final: 0.7917 (m-80) REVERT: A 321 MET cc_start: 0.8801 (mpp) cc_final: 0.8320 (mmm) REVERT: B 202 TYR cc_start: 0.8241 (m-80) cc_final: 0.7916 (m-80) REVERT: B 321 MET cc_start: 0.8797 (mpp) cc_final: 0.8317 (mmm) REVERT: C 2 GLU cc_start: 0.8585 (pm20) cc_final: 0.8312 (pm20) REVERT: C 36 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9021 (mtmm) REVERT: D 98 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8689 (ttmm) REVERT: E 14 ASP cc_start: 0.8497 (t0) cc_final: 0.8266 (t0) REVERT: E 91 LYS cc_start: 0.8792 (tptp) cc_final: 0.8563 (tptp) REVERT: E 97 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: E 105 GLN cc_start: 0.9568 (mm110) cc_final: 0.9286 (mm-40) REVERT: F 114 ILE cc_start: 0.9443 (pt) cc_final: 0.9067 (mt) REVERT: G 2 GLU cc_start: 0.8585 (pm20) cc_final: 0.8311 (pm20) REVERT: G 36 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9017 (mtmm) REVERT: H 98 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8694 (ttmm) REVERT: I 14 ASP cc_start: 0.8622 (t0) cc_final: 0.8245 (t0) REVERT: I 91 LYS cc_start: 0.8896 (tptp) cc_final: 0.8686 (tptp) REVERT: I 105 GLN cc_start: 0.9561 (mm110) cc_final: 0.9270 (mm-40) REVERT: J 122 MET cc_start: 0.8303 (tpp) cc_final: 0.8059 (tpp) outliers start: 39 outliers final: 14 residues processed: 189 average time/residue: 0.5049 time to fit residues: 105.2590 Evaluate side-chains 173 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 158 optimal weight: 30.0000 chunk 99 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.049072 restraints weight = 56349.251| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.99 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15512 Z= 0.121 Angle : 0.633 8.952 21124 Z= 0.313 Chirality : 0.042 0.143 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.919 156.072 2456 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.88 % Allowed : 16.78 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.21), residues: 1654 helix: 2.01 (0.22), residues: 582 sheet: 0.37 (0.25), residues: 416 loop : -0.35 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 93 TYR 0.023 0.001 TYR J 85 PHE 0.008 0.001 PHE D 143 TRP 0.013 0.001 TRP E 70 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00277 (15500) covalent geometry : angle 0.63302 (21124) hydrogen bonds : bond 0.02909 ( 684) hydrogen bonds : angle 4.32991 ( 2091) metal coordination : bond 0.00193 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9246 (ttm) cc_final: 0.8989 (ttp) REVERT: A 202 TYR cc_start: 0.8228 (m-80) cc_final: 0.7865 (m-80) REVERT: A 321 MET cc_start: 0.8787 (mpp) cc_final: 0.8268 (mmm) REVERT: B 1 MET cc_start: 0.9250 (ttm) cc_final: 0.8992 (ttp) REVERT: B 202 TYR cc_start: 0.8223 (m-80) cc_final: 0.7859 (m-80) REVERT: B 321 MET cc_start: 0.8791 (mpp) cc_final: 0.8270 (mmm) REVERT: C 36 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9032 (mtmm) REVERT: C 88 GLU cc_start: 0.7488 (pp20) cc_final: 0.7158 (pp20) REVERT: D 98 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8748 (ttmm) REVERT: E 14 ASP cc_start: 0.8559 (t0) cc_final: 0.8348 (t0) REVERT: E 97 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: E 105 GLN cc_start: 0.9573 (mm110) cc_final: 0.9265 (mm-40) REVERT: F 114 ILE cc_start: 0.9456 (pt) cc_final: 0.9046 (mt) REVERT: G 36 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9025 (mtmm) REVERT: G 88 GLU cc_start: 0.7482 (pp20) cc_final: 0.7149 (pp20) REVERT: H 98 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8756 (ttmm) REVERT: I 14 ASP cc_start: 0.8519 (t0) cc_final: 0.8182 (t0) REVERT: I 105 GLN cc_start: 0.9549 (mm110) cc_final: 0.9252 (mm-40) outliers start: 28 outliers final: 12 residues processed: 179 average time/residue: 0.5227 time to fit residues: 103.1533 Evaluate side-chains 168 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 134 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.073447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050390 restraints weight = 55594.311| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.94 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15512 Z= 0.107 Angle : 0.650 9.973 21124 Z= 0.318 Chirality : 0.042 0.153 2196 Planarity : 0.004 0.053 2562 Dihedral : 12.752 153.869 2456 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.28 % Allowed : 17.52 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.21), residues: 1654 helix: 1.97 (0.22), residues: 582 sheet: 0.42 (0.26), residues: 414 loop : -0.27 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 148 TYR 0.010 0.001 TYR I 94 PHE 0.007 0.001 PHE D 127 TRP 0.014 0.001 TRP E 70 HIS 0.003 0.000 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00238 (15500) covalent geometry : angle 0.65002 (21124) hydrogen bonds : bond 0.02641 ( 684) hydrogen bonds : angle 4.17280 ( 2091) metal coordination : bond 0.00074 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8251 (m-80) cc_final: 0.7883 (m-80) REVERT: A 321 MET cc_start: 0.8739 (mpp) cc_final: 0.8256 (mmm) REVERT: B 202 TYR cc_start: 0.8250 (m-80) cc_final: 0.7881 (m-80) REVERT: B 321 MET cc_start: 0.8739 (mpp) cc_final: 0.8255 (mmm) REVERT: C 36 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9050 (mtmm) REVERT: C 88 GLU cc_start: 0.7395 (pp20) cc_final: 0.6868 (pp20) REVERT: D 98 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8752 (ttmm) REVERT: E 12 GLN cc_start: 0.8943 (mp10) cc_final: 0.8669 (mp10) REVERT: E 14 ASP cc_start: 0.8568 (t0) cc_final: 0.8280 (t0) REVERT: E 97 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: E 105 GLN cc_start: 0.9577 (mm110) cc_final: 0.9293 (mm-40) REVERT: F 114 ILE cc_start: 0.9457 (pt) cc_final: 0.9119 (mt) REVERT: F 122 MET cc_start: 0.8545 (tpp) cc_final: 0.8273 (tpp) REVERT: G 36 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9044 (mtmm) REVERT: G 88 GLU cc_start: 0.7394 (pp20) cc_final: 0.6864 (pp20) REVERT: H 98 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8752 (ttmm) REVERT: I 14 ASP cc_start: 0.8467 (t0) cc_final: 0.8140 (t0) REVERT: I 105 GLN cc_start: 0.9568 (mm110) cc_final: 0.9284 (mm-40) REVERT: J 122 MET cc_start: 0.8252 (tpp) cc_final: 0.7990 (tpp) outliers start: 34 outliers final: 14 residues processed: 196 average time/residue: 0.5177 time to fit residues: 111.6907 Evaluate side-chains 181 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 154 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.071392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047838 restraints weight = 57471.979| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.99 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15512 Z= 0.246 Angle : 0.718 10.554 21124 Z= 0.355 Chirality : 0.044 0.163 2196 Planarity : 0.004 0.051 2562 Dihedral : 12.873 155.108 2456 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.61 % Allowed : 19.06 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.21), residues: 1654 helix: 1.91 (0.22), residues: 582 sheet: 0.39 (0.25), residues: 418 loop : -0.27 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 83 TYR 0.019 0.001 TYR J 85 PHE 0.016 0.001 PHE D 143 TRP 0.015 0.001 TRP I 70 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00563 (15500) covalent geometry : angle 0.71792 (21124) hydrogen bonds : bond 0.03379 ( 684) hydrogen bonds : angle 4.38378 ( 2091) metal coordination : bond 0.00686 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8264 (m-80) cc_final: 0.7895 (m-80) REVERT: A 321 MET cc_start: 0.8808 (mpp) cc_final: 0.8327 (mmm) REVERT: B 202 TYR cc_start: 0.8258 (m-80) cc_final: 0.7902 (m-80) REVERT: B 321 MET cc_start: 0.8815 (mpp) cc_final: 0.8331 (mmm) REVERT: C 36 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9042 (mtmm) REVERT: D 98 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8760 (ttmm) REVERT: E 14 ASP cc_start: 0.8602 (t0) cc_final: 0.8360 (t0) REVERT: E 97 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: E 101 ASP cc_start: 0.9471 (m-30) cc_final: 0.9268 (m-30) REVERT: E 105 GLN cc_start: 0.9583 (mm110) cc_final: 0.9290 (mm110) REVERT: F 74 GLN cc_start: 0.8988 (tp40) cc_final: 0.8666 (tp40) REVERT: F 85 TYR cc_start: 0.7808 (p90) cc_final: 0.7434 (p90) REVERT: F 114 ILE cc_start: 0.9458 (pt) cc_final: 0.9063 (mt) REVERT: G 36 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9034 (mtmm) REVERT: H 98 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8765 (ttmm) REVERT: I 14 ASP cc_start: 0.8499 (t0) cc_final: 0.8221 (t0) REVERT: I 105 GLN cc_start: 0.9572 (mm110) cc_final: 0.9285 (mm-40) REVERT: J 122 MET cc_start: 0.8352 (tpp) cc_final: 0.8054 (tpp) outliers start: 24 outliers final: 13 residues processed: 180 average time/residue: 0.5186 time to fit residues: 102.9848 Evaluate side-chains 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 108 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.071097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047635 restraints weight = 57185.735| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.96 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15512 Z= 0.215 Angle : 0.746 12.316 21124 Z= 0.366 Chirality : 0.044 0.152 2196 Planarity : 0.004 0.053 2562 Dihedral : 12.928 155.971 2456 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.41 % Allowed : 19.66 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.21), residues: 1654 helix: 1.87 (0.22), residues: 582 sheet: 0.32 (0.25), residues: 428 loop : -0.23 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 149 TYR 0.011 0.001 TYR G 69 PHE 0.014 0.001 PHE D 143 TRP 0.014 0.001 TRP I 70 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00493 (15500) covalent geometry : angle 0.74637 (21124) hydrogen bonds : bond 0.03377 ( 684) hydrogen bonds : angle 4.46126 ( 2091) metal coordination : bond 0.00497 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9146 (ttp) cc_final: 0.8893 (ttp) REVERT: A 202 TYR cc_start: 0.8257 (m-80) cc_final: 0.7939 (m-80) REVERT: A 321 MET cc_start: 0.8827 (mpp) cc_final: 0.8476 (mmm) REVERT: B 1 MET cc_start: 0.9149 (ttp) cc_final: 0.8897 (ttp) REVERT: B 202 TYR cc_start: 0.8252 (m-80) cc_final: 0.7933 (m-80) REVERT: B 321 MET cc_start: 0.8834 (mpp) cc_final: 0.8481 (mmm) REVERT: C 36 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9022 (mtmm) REVERT: C 88 GLU cc_start: 0.7526 (pp20) cc_final: 0.7269 (pp20) REVERT: D 98 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8751 (ttmm) REVERT: E 14 ASP cc_start: 0.8593 (t0) cc_final: 0.8382 (t0) REVERT: E 101 ASP cc_start: 0.9466 (m-30) cc_final: 0.9248 (m-30) REVERT: E 105 GLN cc_start: 0.9568 (mm110) cc_final: 0.9273 (mm110) REVERT: F 74 GLN cc_start: 0.9051 (tp40) cc_final: 0.8716 (tp40) REVERT: F 114 ILE cc_start: 0.9454 (pt) cc_final: 0.9100 (mt) REVERT: G 36 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9014 (mtmm) REVERT: G 88 GLU cc_start: 0.7520 (pp20) cc_final: 0.7261 (pp20) REVERT: H 98 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8756 (ttmm) REVERT: I 101 ASP cc_start: 0.9472 (m-30) cc_final: 0.9256 (m-30) REVERT: I 105 GLN cc_start: 0.9555 (mm110) cc_final: 0.9260 (mm110) REVERT: J 122 MET cc_start: 0.8416 (tpp) cc_final: 0.8112 (tpp) outliers start: 21 outliers final: 16 residues processed: 177 average time/residue: 0.5348 time to fit residues: 104.1257 Evaluate side-chains 174 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 0.0980 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.071190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047761 restraints weight = 57427.023| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.98 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15512 Z= 0.193 Angle : 0.753 12.350 21124 Z= 0.369 Chirality : 0.043 0.154 2196 Planarity : 0.004 0.053 2562 Dihedral : 12.909 155.787 2456 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.34 % Allowed : 19.80 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.21), residues: 1654 helix: 1.85 (0.22), residues: 582 sheet: 0.33 (0.25), residues: 428 loop : -0.20 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 149 TYR 0.026 0.001 TYR F 85 PHE 0.012 0.001 PHE D 143 TRP 0.032 0.001 TRP E 174 HIS 0.012 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00445 (15500) covalent geometry : angle 0.75294 (21124) hydrogen bonds : bond 0.03353 ( 684) hydrogen bonds : angle 4.42210 ( 2091) metal coordination : bond 0.00418 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8285 (m-80) cc_final: 0.7953 (m-80) REVERT: A 321 MET cc_start: 0.8811 (mpp) cc_final: 0.8483 (mmm) REVERT: B 202 TYR cc_start: 0.8291 (m-80) cc_final: 0.7962 (m-80) REVERT: B 321 MET cc_start: 0.8815 (mpp) cc_final: 0.8486 (mmm) REVERT: C 36 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9028 (mtmm) REVERT: C 88 GLU cc_start: 0.7432 (pp20) cc_final: 0.7182 (pp20) REVERT: D 98 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8761 (ttmm) REVERT: D 150 THR cc_start: 0.6265 (m) cc_final: 0.5899 (m) REVERT: E 14 ASP cc_start: 0.8607 (t0) cc_final: 0.8354 (t0) REVERT: E 101 ASP cc_start: 0.9476 (m-30) cc_final: 0.9265 (m-30) REVERT: E 105 GLN cc_start: 0.9569 (mm110) cc_final: 0.9264 (mm-40) REVERT: E 174 TRP cc_start: 0.7976 (t-100) cc_final: 0.7346 (t-100) REVERT: F 74 GLN cc_start: 0.9072 (tp40) cc_final: 0.8702 (tp40) REVERT: F 114 ILE cc_start: 0.9513 (pt) cc_final: 0.9122 (mt) REVERT: G 36 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9018 (mtmm) REVERT: G 88 GLU cc_start: 0.7433 (pp20) cc_final: 0.7181 (pp20) REVERT: H 98 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8768 (ttmm) REVERT: H 150 THR cc_start: 0.6307 (m) cc_final: 0.6086 (m) REVERT: I 14 ASP cc_start: 0.8433 (t0) cc_final: 0.8158 (t0) REVERT: I 101 ASP cc_start: 0.9483 (m-30) cc_final: 0.9266 (m-30) REVERT: I 105 GLN cc_start: 0.9558 (mm110) cc_final: 0.9266 (mm110) REVERT: I 174 TRP cc_start: 0.7548 (t-100) cc_final: 0.7345 (t-100) REVERT: J 122 MET cc_start: 0.8412 (tpp) cc_final: 0.8185 (tpp) outliers start: 20 outliers final: 13 residues processed: 176 average time/residue: 0.5107 time to fit residues: 99.6923 Evaluate side-chains 171 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.0050 chunk 147 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.048603 restraints weight = 56679.270| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.96 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15512 Z= 0.137 Angle : 0.732 12.411 21124 Z= 0.358 Chirality : 0.043 0.145 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.775 154.114 2456 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.28 % Allowed : 20.20 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.21), residues: 1654 helix: 1.91 (0.22), residues: 582 sheet: 0.42 (0.25), residues: 422 loop : -0.17 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 149 TYR 0.008 0.001 TYR C 40 PHE 0.008 0.001 PHE A 10 TRP 0.024 0.001 TRP E 174 HIS 0.007 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00319 (15500) covalent geometry : angle 0.73181 (21124) hydrogen bonds : bond 0.02992 ( 684) hydrogen bonds : angle 4.31160 ( 2091) metal coordination : bond 0.00160 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3901.93 seconds wall clock time: 67 minutes 24.21 seconds (4044.21 seconds total)